HEADER TRANSFERASE 24-AUG-12 4GRH TITLE CRYSTAL STRUCTURE OF PABB OF STENOTROPHOMONAS MALTOPHILIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINODEOXYCHORISMATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.6.1.85; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STENOTROPHOMONAS MALTOPHILIA; SOURCE 3 ORGANISM_TAXID: 522373; SOURCE 4 STRAIN: K279A; SOURCE 5 GENE: PABB, SMLT1032; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HELIX-SHEET-HELIX SANDWICH, CHORISMATE, 4-AMINO-4-DEOXYCHORISMATE, KEYWDS 2 PABA, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BERA,V.ATANASOVA,J.E.LADNER,J.F.PARSONS REVDAT 3 13-SEP-23 4GRH 1 REMARK SEQADV LINK REVDAT 2 02-JAN-13 4GRH 1 JRNL REVDAT 1 26-DEC-12 4GRH 0 JRNL AUTH A.K.BERA,V.ATANASOVA,A.DHANDA,J.E.LADNER,J.F.PARSONS JRNL TITL STRUCTURE OF AMINODEOXYCHORISMATE SYNTHASE FROM JRNL TITL 2 STENOTROPHOMONAS MALTOPHILIA. JRNL REF BIOCHEMISTRY V. 51 10208 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23230967 JRNL DOI 10.1021/BI301243V REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 40399 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2147 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5273 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 285 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3354 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 0.23000 REMARK 3 B12 (A**2) : -0.08000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.366 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3620 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4945 ; 2.159 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 7.221 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;35.487 ;23.046 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 537 ;15.577 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;19.874 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.185 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2802 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4GRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0809 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE CRYSTAL REMARK 200 SAGITTAL FOCUSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42573 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 46.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 42.40 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1K0G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MAGNESIUM CHLORIDE, 0.1 M REMARK 280 HEPES, 12-15% W/V PEG550 MME, 0.1% CHAPS, PH 7.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.04450 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.04450 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.04450 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 58.04450 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 58.04450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 58.04450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 697 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 37 REMARK 465 THR A 38 REMARK 465 ALA A 39 REMARK 465 ASP A 285 REMARK 465 ALA A 286 REMARK 465 ALA A 287 REMARK 465 ARG A 288 REMARK 465 ILE A 289 REMARK 465 GLN A 290 REMARK 465 GLU A 291 REMARK 465 LEU A 292 REMARK 465 VAL A 293 REMARK 465 GLY A 294 REMARK 465 HIS A 295 REMARK 465 PRO A 296 REMARK 465 LYS A 297 REMARK 465 GLN A 452 REMARK 465 GLN A 453 REMARK 465 GLY A 454 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 227 O HOH A 677 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 216 CE2 TRP A 216 CD2 0.075 REMARK 500 HIS A 267 CG HIS A 267 CD2 0.055 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 165 CA - CB - CG ANGL. DEV. = 14.7 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 312 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 409 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 409 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 13 140.02 -35.40 REMARK 500 ASP A 67 27.35 44.69 REMARK 500 ASP A 124 0.07 -69.78 REMARK 500 GLU A 145 -13.44 62.74 REMARK 500 LEU A 165 36.83 -86.34 REMARK 500 SER A 167 71.59 54.97 REMARK 500 ALA A 168 -26.29 -149.73 REMARK 500 ALA A 169 -97.44 -160.90 REMARK 500 LEU A 170 54.90 93.57 REMARK 500 GLU A 172 111.03 111.20 REMARK 500 TYR A 333 -122.10 47.78 REMARK 500 THR A 367 -77.59 -126.58 REMARK 500 GLN A 383 -3.24 67.61 REMARK 500 ARG A 409 69.13 -103.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 15P A 501 REMARK 610 15P A 502 REMARK 610 15P A 503 REMARK 610 15P A 504 REMARK 610 CPS A 505 REMARK 610 CPS A 506 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 507 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 284 OD2 REMARK 620 2 HOH A 828 O 171.8 REMARK 620 3 HOH A 829 O 76.0 103.3 REMARK 620 4 HOH A 830 O 94.3 85.3 168.5 REMARK 620 5 HOH A 831 O 80.9 107.3 93.1 91.6 REMARK 620 6 HOH A 832 O 77.9 94.0 79.9 92.0 158.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 15P A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPS A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPS A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 507 DBREF 4GRH A 2 454 UNP B2FR92 B2FR92_STRMK 2 454 SEQADV 4GRH GLY A -2 UNP B2FR92 EXPRESSION TAG SEQADV 4GRH SER A -1 UNP B2FR92 EXPRESSION TAG SEQADV 4GRH HIS A 0 UNP B2FR92 EXPRESSION TAG SEQADV 4GRH GLY A 1 UNP B2FR92 EXPRESSION TAG SEQRES 1 A 457 GLY SER HIS GLY THR HIS ALA PRO LEU ILE HIS PRO LEU SEQRES 2 A 457 PRO HIS PRO ILE ASP LEU LEU ALA LEU GLN GLN HIS ASP SEQRES 3 A 457 PRO ALA ARG PHE PRO LEU LEU MET GLU SER THR ALA SER SEQRES 4 A 457 GLY THR ALA GLN GLY ARG TRP SER LEU LEU LEU VAL ALA SEQRES 5 A 457 GLN GLY ASP GLY LEU ARG LEU ASP ALA ASP GLY GLN VAL SEQRES 6 A 457 ARG ASP GLN HIS ASP LEU VAL GLN PRO GLY THR PHE LEU SEQRES 7 A 457 GLN ALA LEU ASP ARG ALA TRP GLN HIS GLU ARG LEU SER SEQRES 8 A 457 HIS ASP GLY SER HIS SER LEU PRO PHE ARG GLY GLY TRP SEQRES 9 A 457 ALA LEU MET LEU ASP TYR GLU VAL ALA SER GLN ILE GLU SEQRES 10 A 457 PRO VAL LEU PRO ALA ARG ALA ARG GLY ASP GLY ARG PRO SEQRES 11 A 457 THR ALA LEU ALA LEU ARG CYS PRO ALA ALA VAL LEU HIS SEQRES 12 A 457 ASP HIS HIS ASN GLU ALA SER PHE VAL ILE ALA GLU ALA SEQRES 13 A 457 GLY GLU GLN ALA LEU LEU ASP ALA LEU VAL ALA LEU ALA SEQRES 14 A 457 SER ALA ALA LEU PRO GLU ALA GLY GLN GLY TRP GLN PRO SEQRES 15 A 457 PRO GLN ALA VAL GLY GLU ASP ALA PRO GLN ARG PHE THR SEQRES 16 A 457 ASP GLY VAL ARG ARG VAL ILE GLU TYR LEU ARG ALA GLY SEQRES 17 A 457 ASP VAL PHE GLN VAL ASN LEU SER ARG ARG TRP ASN ALA SEQRES 18 A 457 GLN PHE ALA ALA PRO VAL SER PRO GLN ALA LEU TYR ALA SEQRES 19 A 457 GLN LEU ARG ARG ALA ASN PRO ALA PRO PHE ALA GLY LEU SEQRES 20 A 457 PHE SER ALA HIS GLY ARG HIS VAL VAL SER SER SER PRO SEQRES 21 A 457 GLU ARG LEU VAL SER VAL HIS ALA GLY HIS ALA GLN THR SEQRES 22 A 457 ARG PRO ILE ALA GLY THR ARG PRO ARG PHE GLU GLY ASP SEQRES 23 A 457 ASP ASP ALA ALA ARG ILE GLN GLU LEU VAL GLY HIS PRO SEQRES 24 A 457 LYS GLU ARG ALA GLU HIS VAL MET LEU ILE ASP LEU GLU SEQRES 25 A 457 ARG ASN ASP LEU GLY ARG ILE CYS LEU PRO GLY THR VAL SEQRES 26 A 457 VAL VAL ASP GLU LEU MET THR VAL GLU SER TYR ALA HIS SEQRES 27 A 457 VAL HIS HIS ILE VAL SER ASN VAL SER GLY HIS LEU ARG SEQRES 28 A 457 PRO GLU VAL THR PRO GLY GLU VAL ILE ALA ALA THR PHE SEQRES 29 A 457 PRO GLY GLY THR ILE THR GLY CYS PRO LYS VAL ARG CYS SEQRES 30 A 457 MET GLN ILE ILE SER GLU LEU GLU GLN VAL PRO ARG GLY SEQRES 31 A 457 ALA TYR THR GLY ALA PHE GLY TRP LEU ASN ARG ASP GLY SEQRES 32 A 457 ASP LEU ASP LEU ASN ILE LEU ILE ARG THR ALA GLU VAL SEQRES 33 A 457 ASP GLY HIS GLU VAL SER PHE ARG THR GLY ALA GLY ILE SEQRES 34 A 457 VAL VAL ASP SER ASP PRO ASP LYS GLU LEU ASP GLU THR SEQRES 35 A 457 ARG ALA LYS ALA ARG GLY LEU LEU ARG ALA LEU GLY GLN SEQRES 36 A 457 GLN GLY HET 15P A 501 8 HET 15P A 502 8 HET 15P A 503 10 HET 15P A 504 10 HET CPS A 505 36 HET CPS A 506 29 HET MG A 507 1 HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM MG MAGNESIUM ION HETSYN 15P PEG 1500 HETSYN CPS CHAPS FORMUL 2 15P 4(C69 H140 O35) FORMUL 6 CPS 2(C32 H58 N2 O7 S) FORMUL 8 MG MG 2+ FORMUL 9 HOH *232(H2 O) HELIX 1 1 ASP A 15 ASP A 23 1 9 HELIX 2 2 PRO A 24 PHE A 27 5 4 HELIX 3 3 THR A 73 GLU A 85 1 13 HELIX 4 4 VAL A 109 GLU A 114 1 6 HELIX 5 5 GLU A 155 LEU A 165 1 11 HELIX 6 6 ALA A 187 GLY A 205 1 19 HELIX 7 7 SER A 225 ASN A 237 1 13 HELIX 8 8 ASP A 312 ILE A 316 5 5 HELIX 9 9 THR A 352 PHE A 361 1 10 HELIX 10 10 PRO A 370 GLN A 383 1 14 HELIX 11 11 ASP A 431 GLY A 451 1 21 SHEET 1 A11 LEU A 6 PRO A 9 0 SHEET 2 A11 SER A 147 ALA A 151 -1 O ALA A 151 N LEU A 6 SHEET 3 A11 ALA A 136 ASP A 141 -1 N ALA A 137 O ILE A 150 SHEET 4 A11 ARG A 42 VAL A 48 -1 N LEU A 46 O VAL A 138 SHEET 5 A11 LEU A 29 THR A 34 -1 N LEU A 29 O LEU A 47 SHEET 6 A11 ALA A 242 ALA A 247 -1 O ALA A 242 N GLU A 32 SHEET 7 A11 ARG A 250 SER A 254 -1 O SER A 254 N GLY A 243 SHEET 8 A11 THR A 410 ASP A 414 -1 O ALA A 411 N VAL A 253 SHEET 9 A11 GLU A 417 ILE A 426 -1 O SER A 419 N GLU A 412 SHEET 10 A11 GLN A 209 GLN A 219 -1 N VAL A 210 O ILE A 426 SHEET 11 A11 ALA A 182 GLU A 185 -1 N ALA A 182 O GLN A 219 SHEET 1 B11 LEU A 6 PRO A 9 0 SHEET 2 B11 SER A 147 ALA A 151 -1 O ALA A 151 N LEU A 6 SHEET 3 B11 ALA A 136 ASP A 141 -1 N ALA A 137 O ILE A 150 SHEET 4 B11 ARG A 42 VAL A 48 -1 N LEU A 46 O VAL A 138 SHEET 5 B11 LEU A 29 THR A 34 -1 N LEU A 29 O LEU A 47 SHEET 6 B11 ALA A 242 ALA A 247 -1 O ALA A 242 N GLU A 32 SHEET 7 B11 ARG A 250 SER A 254 -1 O SER A 254 N GLY A 243 SHEET 8 B11 THR A 410 ASP A 414 -1 O ALA A 411 N VAL A 253 SHEET 9 B11 GLU A 417 ILE A 426 -1 O SER A 419 N GLU A 412 SHEET 10 B11 GLN A 209 GLN A 219 -1 N VAL A 210 O ILE A 426 SHEET 11 B11 GLY A 368 CYS A 369 -1 O CYS A 369 N GLN A 209 SHEET 1 C12 VAL A 69 GLN A 70 0 SHEET 2 C12 VAL A 62 ASP A 64 -1 N VAL A 62 O GLN A 70 SHEET 3 C12 GLY A 53 LEU A 56 -1 N ARG A 55 O ARG A 63 SHEET 4 C12 ALA A 129 CYS A 134 -1 O ALA A 129 N LEU A 56 SHEET 5 C12 GLY A 100 LEU A 105 -1 N ALA A 102 O LEU A 132 SHEET 6 C12 ALA A 392 ASN A 397 -1 O ALA A 392 N LEU A 105 SHEET 7 C12 LEU A 402 ILE A 406 -1 O ASN A 405 N PHE A 393 SHEET 8 C12 GLU A 258 HIS A 264 -1 N GLU A 258 O ILE A 406 SHEET 9 C12 HIS A 267 GLN A 269 -1 O GLN A 269 N SER A 262 SHEET 10 C12 HIS A 335 HIS A 346 -1 O GLY A 345 N ALA A 268 SHEET 11 C12 VAL A 323 SER A 332 -1 N LEU A 327 O ILE A 339 SHEET 12 C12 ARG A 279 GLU A 281 1 N PHE A 280 O GLU A 331 SHEET 1 D11 VAL A 69 GLN A 70 0 SHEET 2 D11 VAL A 62 ASP A 64 -1 N VAL A 62 O GLN A 70 SHEET 3 D11 GLY A 53 LEU A 56 -1 N ARG A 55 O ARG A 63 SHEET 4 D11 ALA A 129 CYS A 134 -1 O ALA A 129 N LEU A 56 SHEET 5 D11 GLY A 100 LEU A 105 -1 N ALA A 102 O LEU A 132 SHEET 6 D11 ALA A 392 ASN A 397 -1 O ALA A 392 N LEU A 105 SHEET 7 D11 LEU A 402 ILE A 406 -1 O ASN A 405 N PHE A 393 SHEET 8 D11 GLU A 258 HIS A 264 -1 N GLU A 258 O ILE A 406 SHEET 9 D11 HIS A 267 GLN A 269 -1 O GLN A 269 N SER A 262 SHEET 10 D11 HIS A 335 HIS A 346 -1 O GLY A 345 N ALA A 268 SHEET 11 D11 GLU A 301 LEU A 305 1 N VAL A 303 O HIS A 338 LINK OD2 ASP A 284 MG MG A 507 1555 1555 2.25 LINK MG MG A 507 O HOH A 828 1555 1555 2.01 LINK MG MG A 507 O HOH A 829 1555 1555 2.24 LINK MG MG A 507 O HOH A 830 1555 1555 1.96 LINK MG MG A 507 O HOH A 831 1555 1555 2.13 LINK MG MG A 507 O HOH A 832 1555 1555 2.22 CISPEP 1 PHE A 361 PRO A 362 0 1.63 CISPEP 2 CYS A 369 PRO A 370 0 -4.27 SITE 1 AC1 6 LEU A 56 ALA A 58 GLY A 60 GLU A 108 SITE 2 AC1 6 SER A 111 THR A 128 SITE 1 AC2 2 TRP A 43 HOH A 698 SITE 1 AC3 9 ASN A 211 PRO A 278 PHE A 280 THR A 365 SITE 2 AC3 9 ILE A 366 TYR A 389 ARG A 409 GLY A 423 SITE 3 AC3 9 LYS A 442 SITE 1 AC4 5 PRO A 319 VAL A 324 ASP A 325 GLU A 326 SITE 2 AC4 5 VAL A 340 SITE 1 AC5 6 ASP A 15 GLU A 32 ARG A 42 TYR A 230 SITE 2 AC5 6 ALA A 231 ARG A 234 SITE 1 AC6 6 ASP A 284 HOH A 828 HOH A 829 HOH A 830 SITE 2 AC6 6 HOH A 831 HOH A 832 CRYST1 161.300 161.300 116.089 90.00 90.00 120.00 P 63 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006200 0.003579 0.000000 0.00000 SCALE2 0.000000 0.007159 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008614 0.00000